Variant report

Variant	rs4652143
Chromosome Location	chr1:175983994-175983995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10158829	1.00[CHB][hapmap]
rs10436864	0.87[ASN][1000 genomes]
rs10494496	1.00[CHB][hapmap]
rs10737315	0.87[ASN][1000 genomes]
rs10737316	0.82[CHB][hapmap]
rs10753111	0.80[ASN][1000 genomes]
rs10798427	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10798428	0.87[ASN][1000 genomes]
rs10798431	0.82[CHB][hapmap]
rs10913150	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs1155229	0.90[ASN][1000 genomes]
rs11579181	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs11583071	0.87[EUR][1000 genomes]
rs11584481	0.87[CEU][hapmap]
rs11587254	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs11587785	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs11588480	0.86[CEU][hapmap]
rs11590045	0.83[EUR][1000 genomes]
rs11806468	1.00[CHB][hapmap]
rs11809136	1.00[CHB][hapmap]
rs12038027	0.92[ASN][1000 genomes]
rs12239888	0.84[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap]
rs1357337	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1522637	0.82[CHB][hapmap]
rs16849522	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2039231	0.82[CHB][hapmap]
rs2039232	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2481627	0.82[CHB][hapmap]
rs2481641	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2481647	0.82[CHB][hapmap]
rs2481651	0.82[ASN][1000 genomes]
rs2481653	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2481657	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2502822	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2502824	0.82[CHB][hapmap]
rs2502826	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2502832	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs2502834	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs2502835	0.82[CHB][hapmap]
rs2502836	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2502841	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs2502842	0.82[CHB][hapmap]
rs2861629	0.82[CHB][hapmap]
rs3845368	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4129061	0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs4304533	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4307526	0.97[ASN][1000 genomes]
rs4314844	0.92[ASN][1000 genomes]
rs4543747	0.82[CHB][hapmap]
rs4652141	0.81[ASN][1000 genomes]
rs4652142	0.81[ASN][1000 genomes]
rs4652144	0.81[ASN][1000 genomes]
rs4652148	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs4652152	1.00[CHB][hapmap]
rs4652154	0.82[CHB][hapmap]
rs4652155	0.82[CHB][hapmap]
rs553852	0.82[CHB][hapmap]
rs559341	0.82[CHB][hapmap]
rs56949697	0.83[EUR][1000 genomes]
rs599326	0.82[CHB][hapmap]
rs60086820	0.81[ASN][1000 genomes]
rs602933	0.82[CHB][hapmap]
rs6425367	0.87[ASN][1000 genomes]
rs6425368	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6661828	0.87[ASN][1000 genomes]
rs6687043	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6688211	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6704509	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs704827	0.92[CHD][hapmap]
rs73038827	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73038833	0.81[ASN][1000 genomes]
rs7517351	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7521561	1.00[CHB][hapmap]
rs7522442	0.82[CHB][hapmap]
rs7524972	0.92[ASN][1000 genomes]
rs7536464	0.82[CHB][hapmap]
rs7537435	0.87[ASN][1000 genomes]
rs7537480	0.90[ASN][1000 genomes]
rs7539247	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7543769	0.82[CHB][hapmap]
rs7543882	0.81[ASN][1000 genomes]
rs7545043	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7545639	0.90[ASN][1000 genomes]
rs7546538	0.82[ASN][1000 genomes]
rs7552181	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7553184	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs791801	1.00[CHD][hapmap]
rs796933	0.82[CHB][hapmap]
rs9783047	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175946000-175996000	Weak transcription	HMEC	breast
2	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
3	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
6	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:175974000-176003000	Weak transcription	NH-A	brain
8	chr1:175974400-175988200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:175974600-175988800	Weak transcription	Pancreas	Pancrea
10	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:175975400-176003400	Weak transcription	NHLF	lung
12	chr1:175975600-175988400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:175975800-175988800	Weak transcription	Ovary	ovary
14	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
15	chr1:175976400-175996000	Weak transcription	HUVEC	blood vessel
16	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
17	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:175977600-175988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:175978200-175985200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:175978200-175985200	Weak transcription	Fetal Heart	heart
22	chr1:175978200-176001000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:175978200-176003600	Weak transcription	Small Intestine	intestine
24	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
25	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
26	chr1:175978400-175984400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:175978400-175985000	Weak transcription	GM12878-XiMat	blood
28	chr1:175978400-175986800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:175978400-175987800	Weak transcription	Fetal Stomach	stomach
30	chr1:175978400-175988000	Weak transcription	Thymus	Thymus
31	chr1:175978400-175988600	Weak transcription	Esophagus	oesophagus
32	chr1:175978400-175989400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:175978400-175996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:175978400-175996600	Weak transcription	Left Ventricle	heart
35	chr1:175978400-176001600	Weak transcription	Fetal Lung	lung
36	chr1:175978400-176003000	Weak transcription	HSMM	muscle
37	chr1:175978400-176006800	Weak transcription	Fetal Brain Female	brain
38	chr1:175978400-176007000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:175978400-176007000	Weak transcription	Fetal Kidney	kidney
40	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:175978600-176007000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:175978800-175986000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:175978800-175988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:175978800-176003000	Weak transcription	A549	lung
48	chr1:175979200-176011800	Weak transcription	Brain Anterior Caudate	brain
49	chr1:175979400-175994800	Weak transcription	Placenta	Placenta
50	chr1:175979400-176009200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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